I have found a solution to this problem. It is indeed possible to add multiple subnets to a single site via PowerShell.
for ($i = 0; $i -lt $($c.Site).Count; $i++){
$currentSites = Get-ADReplicationSite -Filter *
$currentSubnets = Get-ADReplicationSubnet -Filter *
New-ADReplicationSite -Name $c.Site[$i]
New-ADReplicationSubnet -Name $c.Subnet[$i]
Set-ADReplicationSubnet $c.Subnet[$i] -Site $c.Site[$i]
}
The solution is to first create both the site and the subject and then assign the subnet to the site. This is not possible in the graphical interface. (In the GUI it is mandatory to assign a subnet to a site before exiting the interface)